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2017-10-30ecp-proxy-apps: release number changed to 1.0 (#6049)Abhinav Bhatele1-12/+12
2017-10-30Auto install available pre-built packages from binary cache (#5242)scheibelp5-30/+62
* basic functionality to install spec from a binary cache when it's available; this spiders each cache for each package and could likely be more efficient by caching the results of the first check * add spec to db after installing from binary cache * cache (in memory) spec listings retrieved from binary caches * print a warning vs. failing when no mirrors are configured to retrieve pre-built Spack packages * make automatic retrieval of pre-built spack packages from mirrors optional * no code was using the links stored in the dictionary returned by get_specs, so this simplifies the logic to return only a set of specs * print package prefix after installing from binary cache * provide more information to user on install progress
2017-10-30comd: update the git repo (#6027)Abhinav Bhatele1-2/+2
git repo has moved from exmatex to ECP-copa
2017-10-29Add bowtie2@2.3.0, fix dependencies and sbangs (#5834)George Hartzell2-3/+44
* Add bowtie2@2.3.0, fix dependencies and sbangs Add support for bowtie2@2.3.0 - digest - a patch for 2.3.0 that parallels the existing package. Truth be told it builds (for me) without this, but I'm assuming that they're there for a reason...). - tune up dependencies - need tbb - don't need readline or zlib Several things were installed with sbang's that use `/usr/bin/env` to fine perl or python. Fix the dependency and clean up the sbang lines. * Fix python exe name, avoid path banging I'd cut and pasted the python bit from the perl bit and missed one reference to perl. While I'm there, use the cleaner `spec['perl'].command` instead of banging together the path from its bits. * Fix up the "when" constraints on the dependencies Get the edge cases right. - 2.2.5 doesn't need tbb, 2.3.[01] do. - 2.3.1 needs readline and zlib.
2017-10-29add updated 2017 versions of Intel packages (#5957)Denis Davydov4-0/+8
2017-10-29Changed from setting C compiler to setting C++ compiler (#6011)mmwolf1-2/+2
2017-10-29dealii: remove bzip2 dependency for newer versions (#6022)Denis Davydov1-5/+10
2017-10-28r-iranges: changed url to git and added versioned dependency on r (#5971)Yifan Zhu1-2/+3
2017-10-28r-geomorph and other r fixes (#5961)Audrey Thoma3-0/+53
2017-10-28r-e1071: Add list_url. (#5986)lingnanyuan1-0/+1
2017-10-28likwid: Update checksum (#6007)Michael Kuhn1-1/+1
2017-10-28r-organismdbi: new package (#5997)Yifan Zhu1-0/+50
2017-10-28r-aldex2: Create new package. (#6015)lingnanyuan1-0/+51
2017-10-28legion: add v17.10.0 (#6019)Christoph Junghans1-0/+2
2017-10-28fixing abyss (#5973)Audrey Thoma1-1/+4
2017-10-27Bugfix: from_list_url(). (#5780)Sergey Kosukhin3-1/+65
This fixes a bug in from_list_url where it was referring to a method which no longer exists. This also adds a test for the from_list_url function.
2017-10-27libaec: add v1.0.2 and generic url (#6017)Christoph Junghans1-3/+4
2017-10-27Byobu: new package (#5974)Matthias Diener1-0/+37
2017-10-27ecp-proxy-apps: add more package (#6003)Christoph Junghans1-1/+3
2017-10-27SWFFT: initial commit (#5953)Christoph Junghans1-0/+48
* SWFFT: initial commit * swfft: fix build target * swfft: add v1.0 * Update package.py
2017-10-27comd: add v1.1 (#5994)Christoph Junghans1-6/+6
* comd: add v1.1 * Update package.py * remove serial variant, now ~mpi * Update package.py
2017-10-27r-graph: Create new package. (#5958)lingnanyuan1-0/+37
2017-10-27r-category: Create new package. (#5959)lingnanyuan1-0/+46
2017-10-27r-methodss3: Create new package. (#5960)lingnanyuan1-0/+43
2017-10-27r-oo: Create new package. (#5962)lingnanyuan1-0/+43
2017-10-27r-utils: Create new package. (#5964)lingnanyuan1-0/+38
2017-10-27r-pfam-db: Create new package. (#5965)lingnanyuan1-0/+38
2017-10-27r-oligoclasses: Create new package. (#5966)lingnanyuan1-0/+50
2017-10-27r-interactivedisplaybase: created new package (#5967)Yifan Zhu1-0/+41
2017-10-27r-annotationforge: Create new package. (#5968)lingnanyuan1-0/+46
2017-10-27r-gostats: Create new package. (#5969)lingnanyuan1-0/+46
2017-10-27r-mcmcglmm: new package (#5970)Audrey Thoma2-0/+77
2017-10-27r-annotationhub: created new package (#5972)Yifan Zhu1-0/+51
2017-10-27gnuplot: add 5.2.0 and 5.0.7 (#5979)Denis Davydov1-0/+2
2017-10-27r-deseq2: Create new package. (#5981)lingnanyuan1-0/+53
2017-10-27r-agdex: Create new package. (#5983)lingnanyuan1-0/+39
2017-10-27r-agilp: Create new package. (#5984)lingnanyuan1-0/+36
2017-10-27r-aims: Create new package. (#5987)lingnanyuan1-0/+42
2017-10-27Add info for go@1.9.2 (#5989)George Hartzell1-0/+1
The go team released 1.9.2 which includes fixes for some things that 1.9.1 broke: > ... include fixes to the compiler, linker, runtime, documentation, go command, and the crypto/x509, database/sql, log, and net/smtp packages. They include a fix to a bug introduced in Go 1.9.1 and Go 1.8.4 that broke "go get" of non-Git repositories under certain conditions.
2017-10-27r-annotationfilter: created new package (#5995)Yifan Zhu1-0/+42
2017-10-27r-protgenerics: created new package (#5998)Yifan Zhu1-0/+37
2017-10-26ecp-proxy-apps: add dependencies (#5999)Abhinav Bhatele1-1/+6
2017-10-26miniamr: bump to v1.4.0 (#5975)Christoph Junghans1-12/+8
2017-10-26Package.extends: update semantics when package isn't concrete (#5600)Ben Boeckel1-1/+10
This updates the logic for Package.extends so that if the spec associated with the package is not concrete, it will report true if the package *could extend* the given spec; generally speaking a package could extend a spec as long as none of the details associated with its extendee spec conflict with the given spec. When the spec associated with the package is concrete, this function will only report whether the package *does extend* the given spec. When both the specs are concrete, the semantics are the same as before.
2017-10-26Exodus: skip the -G "Unix Makefiles" part (#5906)Ondřej Čertík2-29/+16
* Exodus: skip the -G "Unix Makefiles" part The problem is that spack passes -G "Unix Makefiles" into cmake, which normally works. But in the Exodus package, it is being passed into a bash wrapper script. In there, the $@ then loses the information about "Unix Makefiles" being just one argument, and in effect passes -G Unix Makefiles into the cmake (without quotes), and so cmake only sees -G Unix, and then fails. This is a known problem with bash with no simple solutions. As a workaround, this patch skips the first two arguments, i.e., -G and "Unix Makefiles". This makes it work. Fixes #5895. * Port exodusii to cmake The cmake options were taken from the cmake-exodus bash script and ported to spack directly. * Use variant forwarding to forward the 'mpi' Now instead of spack install exodusii~mpi^netcdf~mpi^hdf5~mpi one can just use spack install exodusii~mpi
2017-10-26Buildcache: symlinks, externals, & install-checking (#5894)Patrick Gartung4-61/+62
* When creating a tar of a package for a build cache, symlinks are preserved (the corresponding path in the newly-created tarfile will be a symlink rather than a copy of the file) * Dont add external packages to a build cache * When installing from binary cache, don't create install prefix until verification is complete
2017-10-26minife: version bump to v2.1.0 (#5985)Christoph Junghans1-21/+6
2017-10-26Laghos: new package (#5956)Abhinav Bhatele2-0/+64
2017-10-26sw4lite: fix build errors and add variants (#5944)Abhinav Bhatele1-4/+42
* sw4lite: fix build errors and add variants * sw4lite: change linking against blas and lapack * change order of blas and lapack * satisfy flake8 requirements * Update package.py
2017-10-26Customization of the Paraview module file to its nonstandard directory ↵Jon Rood1-0/+12
structure (#5799) * Add the custom paraview lib directory structure to the library paths in the paraview module file. * Fixing flake8 issues. * Checking if lib64 exists for paraview module file generation, else use lib. * Fixing more flake8 problems I introduced.